Ciencias Exactas y Ciencias de la Salud
Permanent URI for this collectionhttps://hdl.handle.net/11285/551039
Pertenecen a esta colección Tesis y Trabajos de grado de las Maestrías correspondientes a las Escuelas de Ingeniería y Ciencias así como a Medicina y Ciencias de la Salud.
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- Exome variant analysis in 40 mexican pulmonary arterial hypertension patients(Instituto Tecnológico y de Estudios Superiores de Monterrey, 2025-12) Sánchez Pichardo, Brenda Eloisa; Treviño Alvarado, Víctor Manuel; emimmayorquin, emipsanchez; Tamez Peña, José Gerardo; Martínez Ledesma, Juan Emmanuel; Sánchez Díaz, Carlos Jerjes; Balderas Martínez, Yalbi Itzel; García Rivas, Gerardo de Jesús; School of Engineering and Sciences; Campus Estado de MéxicoPulmonary arterial hypertension (PAH) is a rare and detrimental disease with a strong genetic component, yet most studies have focused on European or Asian populations. Consequently, little is known about the genetic landscape of PAH in Mexico or whether certain variants have been underrepresented due to ancestry bias in other datasets. This work integrates a set of bioinformatic tools to identify and interpret genetic variants from Whole Exome Sequencing (WES) data of 40 Mexican patients diagnosed with the disease. All patients were recruited by Dr. Carlos Jerjes Díaz Sánchez, the primary clinical col- laborator and data provider for this study. The workflow covered all major steps of data processing, including quality control, read mapping, variant calling, and annotation. These procedures were automated through a custom pipeline implemented in Nextflow, ensuring reproducibility. Subsequently, the analytical phase integrated domain-specific knowledge to interpret variant relevance. First, we systematically examined variants present in 21 PAH-related genes. Second, we explored additional variants based three computational methods: ClinVar annotations, Gene Ontology (GO) terms, and computational predictions. This approach enabled a comprehensive assessment of potential pathogenic variants. Among the 21 PAH-related genes, BMPR2 showed the strongest evidence of pathogenicity, with two variants classified as pathogenic and one of uncertain significance, represent- ing 8% of unrelated individuals. Variants of uncertain significance were also found in eight other PAH-related genes (NOTCH3, EDN1, KCNA5, NOS2, SMAD9, TBX4, and TOPBP1), distributed across 10 of the 39 patients. Additional variants with strong but partially conflicting evidence were identified in HPGDS, TLR4, HSPB9, and other genes. These findings reinforce the central role of BMPR2 in PAH while highlighting po- tential modulatory roles of additional genes involved in inflammation and stress response pathways. Notably, not a single variant was assigned to more than four patients, suggesting that most variants were recently acquired in the family or that those individuals are the first in their families.
- Estimation of ancestry in the mexican population using informative genetic markers(Instituto Tecnológico y de Estudios Superiores de Monterrey, 2024) Valdez Alvarez, Héctor; Treviño Alvarado, Víctor Manuel; emipsanchez; Orozco Orozco, Lorena Sofía; García Ortiz, Humberto; Martínez Ledesma, Juan Emmanuel; Escuela de Ingeniería y Ciencias; Campus Monterrey; Garza Hernández, DeboraThe study of genetic ancestry has become an essential component of modern genetics, offering insights into the origins and migrations of human populations. This thesis presents the development of a genetic ancestry panel specifically tailored for the Mexican population, a group characterized by its high genetic diversity and complex admixture. The primary objective of this research is to accurately estimate the proportions of ancestry in Mexicans using informative genetic markers, thereby addressing the underrepresentation of this population in Genome-Wide Association Studies (GWAS). In the initial phase, various genetic databases were considered, and three were selected for the development of the ancestry panel: the 1000 Genomes Project (1000G), the Human Genome Diversity Project (HGDP), and the Metabolic Analysis in an Indigenous Sample (MAIS). The integration of these datasets provided a comprehensive view of genetic diversity crucial for the panel's accuracy. Principal Component Analysis (PCA) was employed to visualize the genetic structure and verify the separation of ancestral groups. The results confirmed the integrity of the selected datasets. Three methods for selecting Ancestry Informative Markers (AIMs)—Top K, Balanced K, and SumInfo K—were developed and evaluated. Although Balanced K and SumInfo K showed better performance than Top K, integrating Mexican data (MAIS) posed significant challenges, particularly due to the influence of East Asian populations. To address these issues, a revised strategy was implemented, focusing on optimizing AIM selection and improving the robustness of the panel. This involved a detailed workflow and validation process, ensuring the final panel's reliability. Despite the challenges, the new strategy demonstrated promising results, and the final panel is expected to be completed soon. The developed ancestry panel has significant implications for forensic science, personalized medicine, and anthropological research. By accurately estimating ancestry proportions in the Mexican population, this research contributes to a broader understanding of genetic diversity and supports more effective medical and forensic applications. Future work will focus on finalizing the panel and applying it to the oriGen project, which aims to analyze genetic data from a large cohort of Mexicans, further enhancing the understanding of this population's genetic landscape.
- In silico identification of cis-regulatory elements in folate biosynthesis and 1C metabolism genes in plants(Instituto Tecnológico y de Estudios Superiores de Monterrey, 2021-11-26) Salinas Espinosa, Jessica Pamela; TREVIÑO ALVARADO, VICTOR MANUEL; 205076; Treviño Alvarado, Víctor Manuel; puemcuervo; Cuevas Díaz Durán, Raquel; Rodríguez López, Carlos; Martínez Ledesma, Juan Emmanuel; School of Engineering and Sciences; Campus Monterrey; Díaz de la Garza, Rocío IsabelFolates (vitamin B9) are enzyme cofactors required for all organisms for one-carbon (1C) transfer reactions. A deficiency of these nutrients can lead to several health problems. Since humans are not natural producers of folates, the intake of these nutrients from plants is vital for human nutrition. Several techniques that involve the genetic modification of organisms have proved to be effective for the fortify plants with essential macronutrients. However, to achieve this, it is necessary to elucidate the metabolic control in plant systems. Although the genes involved in folate biosynthesis and 1C metabolism in plants are known, the mechanisms of transcriptional regulation have not yet been explored. This project focuses on discovering cis-regulatory DNA elements (motifs) using computational data analysis to provide insights regarding the regulation of folate biosynthesis in plants. For this, we first collected a compendium of known genes related to folate biosynthesis. Then, a database comprising the DNA promoter regions of folate biosynthesis and 1C metabolism genes in 19 different plant species was built and analyzed using different motif discovery algorithms. Afterward, the discovered motifs were tested for statistical significance and further associated with their putative biological role using other bioinformatics tools. A total of 149 statistically significant motifs (p < .05) were discovered in 18 of 19 species using the GimmeMotifs ensemble algorithm. These motifs were represented in 104 different regulatory networks built automatically from co-expression clusters obtained from each plant species. The results from this work could provide an insight into the transcriptional regulation of the folate biosynthesis pathway in plants. Furthermore, the elements found could be used for research in gene editing techniques to produce biofortified crops.